(1) Non-coding RNAs in the process of tumor occurrence, development and stem cell reprogramming;

(2) Theoretical and functional investigation on the complexity of non-coding RNA translation;

(3) New technologies and methods for RNA research;

(4) Non-coding RNAs in the process of centromere and constitutive heterochromatin formation;

(5) Non-coding RNAs during early embryonic development of mice.

(1) Luo, J., and Chen, R^#. (2020). Genetic variations associated with long noncoding RNAs. Essays in Biochemistry 64, 867-873.

(2) Wang, D., Zhou, Z.^#, Wu, E., Ouyang, C., Wei, G., Wang, Y., He, D., Cui, Y., Zhang, D., Chen, X., Reed, S., Luo, J.^#, and Chen, R.^# (2020). LRIK interacts with the Ku70-Ku80 heterodimer enhancing its ability to sense DSBs during NHEJ repair. Cell Death Differ 27(12): 3337-3353. (^#co-corresponding)

(3) Wang, Y.*, Zhu, P.*, Luo, J.*, Wang, J.*, Liu, Z., Wu, W., Du, Y., He, L., Wu, J., He, L., Ye, B., Wang, D., Chen, R.^#, Tian, Y.^#, and Fan, Z.^# (2019). The long noncoding RNA HAND2-AS1 promotes self-renewal of liver cancer stem cells and serves as a potential target for cancer therapy. Embo J 38(17): e101110. (*co-first)

(4) Zhang, Z.*, Jones, A.E.*, Wu, W.*, Kim, J., Kang, Y., Bi, X., Gu, Y., Popov, I.K., Renfrow, M.B., Vassylyeva, M.N., Vassylyev, D.G., Giles, K.E., Chen, D., Kumar, A., Fan, Y., Tong, Y., Liu, C.F., An, W., Chang, C.^#, Luo, J.^#, Chow, L.T.^#, and Wang, H.^# (2017). Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing. Proc Natl Acad Sci U S A 114(38): E7949-E7958. (^#co-corresponding)

(5) Cui, X.*, Zhang, R.*, Yang, Y.*, Wu, E., Tang, Y., Zhao, Z., Li, C., Yang, L., Teng, X., Ye, Y., Cui, Y., Xu, F., Su, Z., Wang, D., Zhang, D., Yang, Y., Sun, J., Luo, J.^#, Zhang, S.^#, Chen, R.^#, and Xi, J.J.^# (2022). Identification and characterization of long non-coding RNA Carip in modulating spatial learning and memory. Cell Rep 38, 110398. (^#co-corresponding)

(6) Yang, B., Zhang, Y., Sun, L., Wang, J., Zhao, Z., Huang, Z., Mao, W., Xue, R., Chen, R., Luo, J.^#, Wang, T.^#, Jiang, J.^#, and Qin, Y.^# (2022). Modulated Ultrasmall γ-Fe2O3 Nanocrystal Assembles for Switchable Magnetic Resonance Imaging and Photothermal-Ferroptotic-Chemical Synergistic Cancer Therapy. Advanced Functional Materials. (^#co-corresponding)

(7) Wu, E.*, Guo, X.*, Teng, X.*, Zhang, R., Li, F., Cui, Y., Zhang, D., Liu, Q., Luo, J.^#, Wang, J.^#, and Chen, R.^# (2021). Discovery of Plasma Membrane-Associated RNAs through APEX-seq. Cell Biochem Biophys. (^#co-corresponding)

(8) Zhang, Q.*, Wu, E.*, Tang, Y.*, Cai, T.*, Zhang, L., Wang, J., Hao, Y., Zhang, B., Zhou, Y., Guo, X., Luo, J.^#, Chen, R.^#, and Yang, F.^# (2021). Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs. Mol Cell Proteomics 20, 100109. (^#co-corresponding)

(9) Li, J.*, Hao, Y.*, Mao, W.*, Xue, X.*, Xu, P., Liu, L., Yuan, J., Zhang, D., Li, N., Chen, H., Zhao, L., Sun, Z.^#, Luo, J.^#, Chen, R.^#, and Zhao, R.^# (2019). LincK contributes to breast tumorigenesis by promoting proliferation and epithelial-to-mesenchymal transition. Journal of Hematology & Oncology 12(1): 19. (^#co-corresponding)

(10) Su, Y.*, Zhang, Y.*, Zhou, M., Zhang, R., Chen, S., Zhang, L., Wang, H., Zhang, D., Zhang, T., Li, X., Zhang, C., Wang, B., Yuan, S., Zhang, M., Zhou, Y., Cao, L., Zhang, M.^#, and Luo, J.^# (2023). Genetic alterations in juvenile cervical clear cell adenocarcinoma unrelated to human papillomavirus. Front Med (Lausanne) 10, 1211888. 10.3389/fmed.2023.1211888. (^#co-corresponding)

(11) Wang, Y.*, Zhu, P.*, Wang, J.*, Zhu, X.*, Luo, J., Meng, S., Wu, J., Ye, B., He, L., Du, Y., He, L., Chen, R.^#, Tian, Y.^#, and Fan, Z.^# (2018). Long noncoding RNA LncHand2 promotes liver repopulation via c-Met signaling. J Hepatol 69 (4): 861-872.

(12) Zhang, C.*, Wang, D.*, Hao, Y.*, Wu, S., Luo, J., Xue, Y., Wang, D., Li, G., Liu, L., Shao, C., Li, H., Yuan, J., Zhu, M., Fu, X.^#, Yang, X.^#, Chen, R.^#, and Teng, Y.^# (2022). LncRNA CCTT-mediated RNA-DNA and RNA-Protein Interactions Facilitate the Recruitment of CENP-C to Centromeric DNA during Kinetochore Assembly. Mol Cell 82(21), 4018-4032.

(13) Liu, L.*, Liu, Z.*, Liu, Q.*, Wu, W.*, Lin, P.*, Liu, X.*, Zhang, Y., Wang, D., Prager, B.C., Gimple, R.C., Yu, J., Zhao, W., Wu, Q., Zhang, W., Wu, E., Chen, X., Luo, J., Rich, J.N.^#, Xie, Q.^#, Jiang, T.^#, and Chen, R.^# (2023). LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2'-O-methylation. Nat Commun 14, 7526. 10.1038/s41467-023-43113-5.

(14) Yan, X.*^#, Zhang, D.*, Wu, W., Wu, S., Qian, J., Hao, Y., Yan, F., Zhu, P., Wu, J., Huang, G., Huang, Y., Luo, J., Liu, X., Liu, B., Chen, X., Du, Y., Chen, R.^#, and Fan, Z.^# (2017). Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA-MUF Interaction with ANXA2 and miR-34a. Cancer Res 77(23): 6704-6716.

(15) Wang, Y.*, He, L.*, Du, Y., Zhu, P., Huang, G., Luo, J., Yan, X., Ye, B., Li, C., Xia, P., Zhang, G., Tian, Y., Chen, R.^#, and Fan, Z.^# (2015). The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling. Cell Stem Cell 16(4): 413-425.

(16) Cai, T.*^#, Zhang, Q.*, Wu, B.*, Wang, J., Li, N., Zhang, T., Wang, Z., Luo, J., Guo, X., Ding, X., Xie, Z., Niu, L., Ning, W., Fan, Z., Chen, X., Guo, X., Chen, R., Zhang, H.^#, and Yang, F.^# (2021). LncRNA-encoded microproteins: A new form of cargo in cell culture-derived and circulating extracellular vesicles. J Extracell Vesicles 10, e12123.

(17) Zhang, Y.W., Wang, Z., Xie, W., Cai, Y., Xia, L., Easwaran, H., Luo, J., Yen, R.C., Li, Y., and Baylin, S.B.^# (2017). Acetylation Enhances TET2 Function in Protecting against Abnormal DNA Methylation during Oxidative Stress. Mol Cell 65(2): 323-335.

(18) Zhang, N.*, Zhao, Z.*, Zhao, Y.*, Yang, L.*, Xue, Y., Feng, Y., Luo, J., Chen, R., Wei, W., and Qin, Y.^# (2023). TGF-beta changes cyto/mito-ribosome balance to target respiratory chain complex V biogenesis in pulmonary fibrosis therapy. Signal Transduct Target Ther 8, 136. 10.1038/s41392-023-01370-2.

(19) Wan, L.*, Hu, P.*, Zhang, L.*, Wang, Z.X.*, Fleming, J., Ni, B., Luo, J., Guan, C.X., Bai, L., Tan, Y., Liu, H., Li, N., Xiao, T., Bai, H., Zhang, Y.A., Zhang, X.E., Wan, K.^#, Bi, L.^#, Ouyang, S.^#, and Zhang, H.^# (2023). Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene. Commun Biol 6, 156. 10.1038/s42003-023-04433-w.

(20) Wu, S.*, Wu, E.*, Wang, D.*, Niu, Y., Yue, H., Zhang, D., Luo, J.^#, and Chen, R.^# (2020). LncRNA HRCEG, regulated by HDAC1, inhibits cells proliferation and epithelial-mesenchymal-transition in gastric cancer. Cancer Genet 241: 25-33. (^#co-corresponding)

(21) Zhang, C., Wu, W., Zhu, H., Yu, X., Zhang, Y., Ye, X., Cheng, H., Ma, R., Cui, H., Luo, J.^#, Guan, J.^#, and Chang, X.^# (2018). Knockdown of long non-coding RNA CCDC144NL-AS1 attenuates migration and invasion phenotypes in endometrial stromal cells from endometriosis. Biol Reprod 100(4): 939-949. (^#co-corresponding)

(22) Hao, Y.*, Yang, X.*, Zhang, D., Luo, J.^#, and Chen, R.^# (2017). Long noncoding RNA LINC01186, regulated by TGF-beta/SMAD3, inhibits migration and invasion through Epithelial-Mesenchymal-Transition in lung cancer. Gene 608: 1-12. (^#co-corresponding)

(23) Liu, L.*, Yue, H.*, Liu, Q.*, Yuan, J.*, Li, J., Wei, G., Chen, X., Lu, Y., Guo, M., Luo, J.^#, and Chen, R.^# (2016). LncRNA MT1JP functions as a tumor suppressor by interacting with TIAR to modulate the p53 pathway. Oncotarget 7(13): 15787-15800. (^#co-corresponding)

(24) Zhang, B.*, Wang, D.*, Wu, J.*, Tang, J., Chen, W., Chen, X., Zhang, D., Deng, Y., Guo, M., Wang, Y.^#, Luo, J.^#, and Chen, R.^# (2016). Expression profiling and functional prediction of long noncoding RNAs in nasopharyngeal nonkeratinizing carcinoma. Discov Med 21(116): 239-250. (^#co-corresponding)

(25) Luo, J.*, Deng, X.*, Buehl, C., Xu, X., and Kuo, M.H.^# (2016). Identification of Tension Sensing Motif of Histone H3 in Saccharomyces cerevisiae and Its Regulation by Histone Modifying Enzymes. Genetics 204(3): 1029-1043. (*co-first)

(26) Luo, J., Xu, X., Hall, H., Hyland, E.M., Boeke, J.D., Hazbun, T., and Kuo, M.H.^# (2010). Histone h3 exerts a key function in mitotic checkpoint control. Mol Cell Biol 30(2): 537-549.  

(27) Liu, J.*, An, Z.*, Luo, J., Li, J., Li, F.^#, and Zhang, Z.^# (2020). Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite. Bioinformatics 36(7): 2033-2039.

(28) Lai, C.*, Liu, L.*^#, Liu, Q.*, Wang, K.*, Cheng, S.*, Zhao, L., Xia, M., Wang, C., Duan, Y., Zhang, L., Liu, Z., Luo, J., Wang, X.^#, Chen, R.^#, and Yang, P.^# (2021). Long noncoding RNA AVAN promotes antiviral innate immunity by interacting with TRIM25 and enhancing the transcription of FOXO3a. Cell Death Differ 28, 2900-2915.

(29) Wan, L.*, Hu, P.*, Zhang, L.*, Wang, Z.X.*, Fleming, J., Ni, B., Luo, J., Guan, C.X., Bai, L., Tan, Y., Liu, H., Li, N., Xiao, T., Bai, H., Zhang, Y.A., Zhang, X.E., Wan, K., Bi, L.^#, Ouyang, S.^#, and Zhang, H.^# (2023). Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene. Commun Biol 6, 156. 10.1038/s42003-023-04433-w.

(30) Du, Z.*, Wen, X.*, Wang, Y.*, Jia, L.*, Zhang, S., Liu, Y., Zhou, L., Li, H., Yang, W., Wang, C., Chen, J., Hao, Y., Salgado Figueroa, D., Chen, H., Li, D., Chen, N., Celik, I., Zhu, Y., Yan, Z., Fu, C., Liu, S., Jiao, B., Wang, Z., Zhang, H., Gulsoy, G., Luo, J., Qin, B., Gao, S., Kapranov, P., Esteban, M.A., Zhang, S., Li, W., Ay, F., Chen, R., Hoffman, A.R.^#, Cui, J.^#, and Hu, J.F.^# (2021). Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biol 22, 233.

(31) Tian, Y.*, Yang, B.*, Qiu, W., Hao, Y., Zhang, Z., Yang, B., Li, N., Cheng, S., Lin, Z., Rui, Y.C., Cheung, O.K.W., Yang, W., Wu, W.K.K., Cheung, Y.S., Lai, P.B.S., Luo, J., Sung, J.J.Y., Chen, R., Wang, H.Y., Cheng, A.S.L.^#, and Yang, P.^# (2019). ER-residential Nogo-B accelerates NAFLD-associated HCC mediated by metabolic reprogramming of oxLDL lipophagy. Nat Commun 10(1): 3391.

(32) Buehl, C.J., Deng, X., Luo, J., Buranasudja, V., Hazbun, T., and Kuo, M.H.^# (2018). A Failsafe for Sensing Chromatid Tension in Mitosis with the Histone H3 Tail in Saccharomyces cerevisiae. Genetics 208(2): 565-578.

(33) Hao, Y.*, Zhang, L.*, Niu, Y., Cai, T., Luo, J., He, S., Zhang, B., Zhang, D., Qin, Y., Yang, F., and Chen, R.^# (2018). SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. Brief Bioinform 19(4): 636-643.

(34) Cui, Y.*, Chen, X.*, Niu, Y.*, Wang, D., Luo, H., Fan, Z., Wang, D., Wu, W., Teng, X., He, S., Luo, J., and Chen, R.^# (2018). Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data. Brief Bioinform 19(6): 1302-1309.

(35) Wang, Z.*, Hao, Y.*, Zhang, C.*, Wang, Z., Liu, X., Li, G., Sun, L., Liang, J., Luo, J., Zhou, D., Chen, R.^#, and Jiang, T.^# (2017). The landscape of viral expression reveals clinically relevant viruses with potential capability of promoting malignancy in lower grade glioma. Clin Cancer Res 23(9): 2177-2185.

(36) Sun, Y.*, Wei, G.*, Luo, H.*, Wu, W.*, Skogerbo, G., Luo, J., and Chen, R.^# (2017). The long noncoding RNA SNHG1 promotes tumor growth through regulating transcription of both local and distal genes. Oncogene 36(49): 6774-6783.

(37) Fan, Z.*, Chen, X.*, Liu, L.*, Zhu, C., Xu, J., Yin, X., Sheng, Y., Zhu, Z., Wen, L., Zuo, X., Zheng, X., Zhang, Y., Xu, J., Huang, H., Zhou, F., Sun, L., Luo, J., Zhang, D., Chen, X., Cui, Y., Hao, Y., Cui, Y.^#, Zhang, X.^#, and Chen, R.^# (2020). The polymorphism rs13259960 in SLEAR predisposes to systemic lupus erythematosus. Arthritis Rheumatol 72(6): 985-996.

(38) Zhang, S.*, Wang, Y.*, Jia, L.*, Wen, X.*, Du, Z.*, Wang, C., Hao, Y., Yu, D., Zhou, L., Chen, N., Chen, J., Chen, H., Zhang, H., Celik, I., Gulsoy, G., Luo, J., Qin, B., Cui, X., Liu, Z., Zhang, S., Esteban, M.A., Ay, F., Xu, W., Chen, R., Li, W., Hoffman, A.R.^#, Hu, J.F.^#, and Cui, J.^# (2019). Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing. Genome Res 29, 1521-1532.

(39) Zhang, C., Wu, W., Ye, X., Ma, R., Luo, J., Zhu, H.^#, and Chang, X.^# (2019). Aberrant expression of CHL1 gene and long non-coding RNA CHL1-AS1, CHL1-AS2 in ovarian endometriosis. Eur J Obstet Gynecol Reprod Biol 236, 177-182.

(40) Hao, Y., Luo, J., Zhang, B., and Chen, R.^# (2017). The Complexity of RNA Translation: Non-translation, Part-translation, De Novo-translation and Over-translation. Prog Biochem Biophys 44(7): 547-556.

(41) Chen, X.*, Hao, Y.*, Cui, Y.*, Fan, Z., He, S., Luo, J., and Chen, R.^# (2017). LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics 33(1): 112-118.

(42) Zhu, L., Tan, X., Liu, W., Mao, F., Wu, C., Zhou, J., Liu, X., Lu, S., Ma, K., Yin, B., Luo, J., Yuan, J., Qiang, B., Chen, R.^#, and Peng, X.^# (2017). Identification and analysis of intermediate-size noncoding RNAs in the rhesus macaque fetal brain. J Genet Genomics 44, 171-174.

(43) Zeng, Z., Zhou, Z.^#, Wang, D., Wang, Z., Yang, H., Luo, J., and Chen, R.^# (2016). Generating a long DNA fragment of the target ncRNA for quantitative polymerase chain reaction by combining ncRNA-oligos hybridization and oligos ligation. J Biotechnol 217: 41-48.

(44) Cui, Y.*, Chen, X.*, Luo, H., Fan, Z., Luo, J., He, S., Yue, H., Zhang, P., and Chen, R.^# (2016). BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications. Bioinformatics 32(11): 1740-1742.

(45) Hao, Y.*, Wu, W.*, Li, H., Yuan, J., Luo, J., Zhao, Y., and Chen, R.^# (2016). NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. Database (Oxford) 2016.

(46) Zhang, C., Guan, J., Luo, J., Wu, W., Ye, X., Cheng, H., Ma, R., Cui, H., and Chang, X.^# (2016). The expression of long non-coding RNA CHL1-AS2 in ovarian endometriosis. Chin J Clin Obstet Gynecol 17(1): 4.

(47) Yuan, J.*, Yue, H.*, Zhang, M., Luo, J., Liu, L., Wu, W., Xiao, T., Chen, X., Chen, X., Zhang, D., Xing, R., Tong, X., Wu, N., Zhao, J.^#, Lu, Y.^#, Guo, M.^#, and Chen, R.^# (2016). Transcriptional profiling analysis and functional prediction of long noncoding RNAs in cancer. Oncotarget 7(7): 8131-8142.

(48) Chen, J., Liu, L., Wei, G., Wu, W., Luo, H., Yuan, J., Luo, J., and Chen, R.^# (2016). The long noncoding RNA ASNR regulates degradation of Bcl-2 mRNA through its interaction with AUF1. Sci Rep 6: 32189.

(49) Luo, H.*, Sun, Y.*, Wei, G.*, Luo, J., Yang, X., Liu, W., Guo, M., and Chen, R.^# (2015). Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells. Biochemistry 54(18): 2895-2902.

(50) Xu, D., Wei, G., Lu, P., Luo, J., Chen, X., Skogerbo, G., and Chen, R.^# (2014). Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy. Protein & cell 5(10): 770-782.